The source tree

From Genomewiki

The source tree is the collection of all code used by the genome browser group: the browser itself but also tons of other tools that are needed to generate genome annotations. You can find information in the help pages on how to install it and in this wiki for Debian/Ubuntu.

"If you can conceive of a bioinformatics job that could be done, it probably already has been done in the kent source tree."
(Hiram)

"The truth is in the source" (slightly adapted from Angie's "Chains Nets"-article)

The intent of this page is just to give an impression of the source tree's layout. See Implementation_Notes for details about the programs.

Tools to explore the source tree:

you can use ctags to index the source tree

and use cscope to search in the source tree (any better ideas for searching?)

Use the bash construct "2>&1" if you want to pipe help messages to less. By default help goes to stderr and goes off the screen quickly. Example: overlapSelect | less does not work, overlapSelect 2>&1 | less is a better idea.

Tools and scripts (!) that were used to load data into the databases. Most of them in subdirs here in the format hgLoadx with x for maf/bed/wiggle/axt/net/chain/out/etc. If you understand these, you can build your own genome browser. :-) Here are also the trackDb.ra-files, something like a list of all tracks, their descriptions and instructions on how to display them.